Having FLAC support was one of my car requirements.
I've Samsung FIT Plus 256 GB with nothing but FLACs and it works OK. It reads meta data properly and picks album covers if present.
Few notes:
- I didn't test a single FLAC file + CUE for storing multiple tracks (can BMW detect them as separated tracks?)
- When browsing albums all tracks without meta data are mixed in a single Unknown Album (could be grouped by directory or sth)
- BMW doesn't refresh meta data of files once indexed. I got few tracks without meta data, I took flash drive home, fixed up meta data, got it back, BMW still didn't see them. I had to rename directory and/or files.